Summary Ciliopathies are a diverse class of developmental diseases that can manifest as defects in kidney, skeletal, eye, heart, reproductive, or mental function. Many ciliopathies, including Bardet-Biedl, Joubert, and Meckel Gruber Syndromes, are caused by defects in the major protein complexes that characterize the ciliary compartment. At least 1,000 proteins are associated with cilia biogenesis and function; uncovering the principles of ciliary protein organization thus requires a large scale, systematic investigation. Our current human protein complex maps, while extensive, have only moderate coverage of ciliary proteins, warranting the collection of targeted experimental datasets. I will use comparative proteomic analysis of cilia from multiple organisms to determine deeply conserved protein-protein interactions likely to be critical to ciliary function in humans. Examining human biological systems in the context of their level of conservation across species is a productive route to distinguish biological signal from noise. My preliminary data on three ciliated species confirm that this approach is capable of identifying conserved ciliary protein complexes. If a pair of proteins are found in physical contact in diverse species, having survived speciation events and gene loss, it can be predicted that this physical interaction is important. First, using mass spectrometry, we will experimentally detect protein complexes within the cilia across a spectrum of eukaryotic organisms, broadly defining conserved ciliary proteins. Second, we will integrate our own experimental data, some of which we have already collected, with outside data to construct a system-wide map of conserved ciliary protein complexes. These conserved ciliary protein complexes are strongly predicted to be functionally important in humans, and potentially involved in human birth defects. Finally, we will test a targeted subset of proteins predicted to associate with known birth defect proteins in vivo using Xenopus laevis embryos as a model system. We have four candidate genes in hand, and will consider candidates from the prior aims as appropriate. This project will lead to a map of critical conserved ciliary protein complexes, a future primary resource for research into diverse ciliopathies.